Variant report

Variant	rs2421095
Chromosome Location	chr2:73113524-73113525
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr2:73113516-73114346	A549	lung:	n/a	n/a
2	CEBPB	chr2:73113492-73114201	MCF-7	breast:	n/a	n/a
3	CEBPB	chr2:73113465-73114312	HCT-116	colon:	n/a	n/a
4	CTCF	chr2:73113444-73115661	A549	lung:	n/a	chr2:73115126-73115142 chr2:73115127-73115140 chr2:73115125-73115143 chr2:73114493-73114506 chr2:73115127-73115140 chr2:73114232-73114245

Variant related genes	Relation type
SPR	TF binding region

Extended variants
information (count: 62 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10211019	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1027848	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1032982	1.00[CHB][hapmap]
rs10496186	0.91[CEU][hapmap]
rs10865393	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11126385	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1150500	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1161265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1161266	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1161267	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11676555	1.00[CHB][hapmap]
rs11679683	1.00[CHB][hapmap]
rs11894160	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12474728	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12622275	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12713775	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12989141	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12996406	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs13035731	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1396106	0.82[EUR][1000 genomes]
rs1508061	1.00[CHB][hapmap]
rs1567230	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17503444	1.00[CHB][hapmap]
rs1911690	1.00[CHB][hapmap]
rs1995734	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs2048170	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2048171	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs2135985	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2420880	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2420881	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2420883	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4321391	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4852298	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]
rs4852891	1.00[CHB][hapmap]
rs4852893	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4852902	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6546781	1.00[CHB][hapmap]
rs6546782	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs6546783	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs6546786	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6546788	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6546789	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6546790	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6546791	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6546792	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6730083	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6739002	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6750740	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6758431	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6758542	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7580268	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs7586787	0.97[EUR][1000 genomes]
rs7588400	1.00[CHB][hapmap]
rs7588602	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7592155	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs925146	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs925147	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs925148	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs990569	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834259	chr2:72941118-73114106	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv532723	chr2:73088191-73219259	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	esv3377861	chr2:73113469-73116017	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2421095	CYP26B1	cis	Whole Blood	GTEx
rs2421095	MPHOSPH10	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73112800-73114000	Enhancers	Placenta	Placenta
2	chr2:73113200-73113600	Enhancers	Hela-S3	cervix
3	chr2:73113200-73113800	Enhancers	Liver	Liver
4	chr2:73113400-73113600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
5	chr2:73113400-73113600	Enhancers	HepG2	liver
6	chr2:73113400-73114000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links